01 - Analysis 1
Selin Jessa
23 May, 2020
1 Configuration
Configuration of project directory & analysis outputs:
Show full config
library(here)## here() starts at /Users/selinjessa/Repos/rrsource(here("rr_helpers.R"))
# Set up outputs
# ...determines name of the subfolder of `outputs` and `figures`
doc_id <- "01"
# ...specify where to save outputs
out <- here("output", doc_id); dir.create(out, recursive = TRUE)
figout <- here("figures", doc_id, "/")
cache <- paste0("~/tmp/", basename(here()), "/", doc_id, "/")The root directory of this project is:
## /Users/selinjessa/Repos/rrOutputs and figures will be saved at these paths, relative to project root:
## rr/output/01## rr/figures/01//2 Overview
This is an example of the first analysis in a project.
3 Libraries
library(ggplot2)
library(tidyverse)Here is a note to self. This markdown code is contained in a check, with visibility controlled by the echo chunk option.
Change echo to TRUE or FALSE to display/hide this chunk.
4 Analysis
4.1 Part 1
This part of the analysis generates a figure; we can use the chunk option echo_fig = TRUE to print its output path.
mtcars %>%
ggplot(aes(x = mpg, y = cyl)) +
geom_point() +
theme_bw()
[figure @ rr/figures/01//pressure…]
4.2 Part 2
This part of the analysis saves the mtcars dataset from R as a TSV. By matching the chunk name to the output file name, we can then use the echo_out = TRUE chunk option to show the path to the file.
head(mtcars)rr_write_tsv(df = mtcars,
path = file.path(out, "mtcars.tsv"),
desc = "The mtcars dataset, verbatim")## rr/output/01/mtcars.tsv info:## ...writing description to rr/output/01/mtcars.desc
[output @ rr/output/01/mtcars.tsv]
5 Reproducibility
This document was last rendered on:
## 2020-05-23 23:59:40The git repository and last commit:
## Local: master /Users/selinjessa/Repos/rr
## Remote: master @ origin (git@github.com:sjessa/rr.git)
## Head: [c2562c5] 2020-05-24: Update HTML with repository infoSession info:
## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.0.0 beta (2020-04-12 r78209)
## os macOS Catalina 10.15.3
## system x86_64, darwin17.0
## ui X11
## language (EN)
## collate en_CA.UTF-8
## ctype en_CA.UTF-8
## tz America/Montreal
## date 2020-05-23
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date lib source
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## crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
## DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.0)
## dbplyr 1.4.2 2019-06-17 [1] CRAN (R 4.0.0)
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## ggplot2 * 3.3.0 2020-03-05 [1] CRAN (R 4.0.0)
## git2r 0.27.1 2020-05-03 [1] CRAN (R 4.0.0)
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## gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0)
## haven 2.2.0 2019-11-08 [1] CRAN (R 4.0.0)
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## httr 1.4.1 2019-08-05 [1] CRAN (R 4.0.0)
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## knitr 1.28 2020-02-06 [1] CRAN (R 4.0.0)
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## lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0)
## lubridate 1.7.8 2020-04-06 [1] CRAN (R 4.0.0)
## magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
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## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
## pkgload 1.0.2 2018-10-29 [1] CRAN (R 4.0.0)
## prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
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## ps 1.3.2 2020-02-13 [1] CRAN (R 4.0.0)
## purrr * 0.3.3 2019-10-18 [1] CRAN (R 4.0.0)
## R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
## Rcpp 1.0.4.6 2020-04-09 [1] CRAN (R 4.0.0)
## readr * 1.3.1 2018-12-21 [1] CRAN (R 4.0.0)
## readxl 1.3.1 2019-03-13 [1] CRAN (R 4.0.0)
## remotes 2.1.1 2020-02-15 [1] CRAN (R 4.0.0)
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## scales 1.1.0 2019-11-18 [1] CRAN (R 4.0.0)
## sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
## stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0)
## stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.0.0)
## testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.0)
## tibble * 3.0.0 2020-03-30 [1] CRAN (R 4.0.0)
## tidyr * 1.0.2 2020-01-24 [1] CRAN (R 4.0.0)
## tidyselect 1.0.0 2020-01-27 [1] CRAN (R 4.0.0)
## tidyverse * 1.3.0 2019-11-21 [1] CRAN (R 4.0.0)
## usethis 1.6.0 2020-04-09 [1] CRAN (R 4.0.0)
## vctrs 0.2.4 2020-03-10 [1] CRAN (R 4.0.0)
## withr 2.1.2 2018-03-15 [1] CRAN (R 4.0.0)
## xfun 0.13 2020-04-13 [1] CRAN (R 4.0.0)
## xml2 1.3.1 2020-04-09 [1] CRAN (R 4.0.0)
## yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.0)
##
## [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
A project of the Kleinman Lab at McGill University.